cram_pipeline.py

import argparse
from multiprocessing import Pool
import cram_utils

parser = argparse.ArgumentParser()
parser.add_argument("-c", "--cores", type=str)
parser.add_argument("-i", "--indir", type=str)
parser.add_argument("-s", "--sample", type=str)
parser.add_argument("-l", "--limit", default=False, action="store_true")

args = parser.parse_args()

cores = args.cores
indir = args.indir
sample = args.sample
limit = args.limit

######################################################

cram_utils.cram_fastq_split_by_lines(indir, sample, cores, 4e7)

######################################################

parts = cram_utils.find_sub_fastq_parts(indir, sample)
args = [(indir, sample, part, limit) for part in parts]

pool = Pool(int(cores))
results = pool.starmap(cram_utils.extract_trimmed_fastq_pairs, args)
pool.close()
pool.join()

"""
######################################################

bc_umi_utils.aggregate_dicts(indir,sample,'anchors')
bc_umi_utils.aggregate_dicts(indir,sample,'targets')

bc_umi_utils.aggregate_stat_dicts(indir,sample,'adapter_edits')

######################################################

qc_pdf_file = f'{indir}/{sample}/{sample}_QC.pdf'

if os.path.isfile(qc_pdf_file):
    print(qc_pdf_file,' exists, skip')
else:
    qc_pdfs = PdfPages(qc_pdf_file)
    bc_umi_utils.whitelist_rankplot(indir,sample,'anchors',qc_pdfs,max_anchors)
    bc_umi_utils.whitelist_rankplot(indir,sample,'targets',qc_pdfs,max_targets)
    qc_pdfs.close()

"""